The couple had been together since meeting on the set of "Hope & Faith" in 2004, when Green was 30 and Fox just 18, reported Us magazine.
"Megan has separated from Brian. They decided on it six months ago," a source said.
The former couple are parents to two sons - Noah, two, and Bodhi, 18 months - but have not been seen in public together since June 9.
It has been rumoured that the pair have quarrelled about her career, with Megan, 29 frequently away making movies.
Their representatives have not yet officially commented on their recent split.